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Catara V, Cubero J, Pothier JF, Bosis E, Bragard C, Đermić E, Holeva MC, Jacques MA, Petter F, Pruvost O, Robène I, Studholme DJ, Tavares F, Vicente JG, Koebnik R, Costa J. Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary Regulated Xanthomonas. Microorganisms 2021; 9:862. [PMID: 33923763 PMCID: PMC8073235 DOI: 10.3390/microorganisms9040862] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 11/17/2022] Open
Abstract
Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis.
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Affiliation(s)
- Vittoria Catara
- Department of Agriculture, Food and Environment, University of Catania, 95125 Catania, Italy
| | - Jaime Cubero
- National Institute for Agricultural and Food Research and Technology (INIA), 28002 Madrid, Spain;
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), 8820 Wädenswil, Switzerland;
| | - Eran Bosis
- Department of Biotechnology Engineering, ORT Braude College of Engineering, Karmiel 2161002, Israel;
| | - Claude Bragard
- UCLouvain, Earth & Life Institute, Applied Microbiology, 1348 Louvain-la-Neuve, Belgium;
| | - Edyta Đermić
- Department of Plant Pathology, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia;
| | - Maria C. Holeva
- Benaki Phytopathological Institute, Scientific Directorate of Phytopathology, Laboratory of Bacteriology, GR-14561 Kifissia, Greece;
| | - Marie-Agnès Jacques
- IRHS, INRA, AGROCAMPUS-Ouest, Univ Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France;
| | - Francoise Petter
- European and Mediterranean Plant Protection Organization (EPPO/OEPP), 75011 Paris, France;
| | - Olivier Pruvost
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France; (O.P.); (I.R.)
| | - Isabelle Robène
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France; (O.P.); (I.R.)
| | | | - Fernando Tavares
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal; or
- FCUP-Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | | | - Ralf Koebnik
- Plant Health Institute of Montpellier (PHIM), Univ Montpellier, Cirad, INRAe, Institut Agro, IRD, 34398 Montpellier, France;
| | - Joana Costa
- Centre for Functional Ecology-Science for People & the Planet, Department of Life Sciences, University of Coimbra, 300-456 Coimbra, Portugal
- Laboratory for Phytopathology, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
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Mendes RJ, Luz JP, Santos C, Tavares F. CRISPR genotyping as complementary tool for epidemiological surveillance of Erwinia amylovora outbreaks. PLoS One 2021; 16:e0250280. [PMID: 33861806 PMCID: PMC8051791 DOI: 10.1371/journal.pone.0250280] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/02/2021] [Indexed: 12/12/2022] Open
Abstract
Fire blight is a destructive plant disease caused by Erwinia amylovora affecting pome fruit trees, and responsible for large yield declines, long phytosanitary confinements, and high economic losses. In Portugal, the first major fire blight outbreaks occurred in 2010 and 2011, and although later considered eradicated, the emergence of other outbreaks in recent years stressed the need to characterize the E. amylovora populations associated with these outbreaks. In this regard, CRISPR genotyping, assessment of three virulence markers, and semi-quantitative virulence bioassays, were carried out to determine the genotype, and assess the virulence of thirty-six E. amylovora isolates associated with outbreaks occurring between 2010 and 2017 and affecting apple and pear orchards located in the country central-west, known as the main producing region of pome fruits in Portugal. The data gathered reveal that 35 E. amylovora isolates belong to one of the widely-distributed CRISPR genotypes (5-24-38 / D-a-α) regardless the host species, year and region. Ea 680 was the single isolate revealing a new CRISPR genotype due to a novel CR2 spacer located closer to the leader sequence and therefore thought to be recently acquired. Regarding pathogenicity, although dot-blot hybridization assays showed the presence of key virulence factors, namely hrpL (T3SS), hrpN (T3E) and amsG from the amylovoran biosynthesis operon in all E. amylovora isolates studied, pathogenicity bioassays on immature pear slices allowed to distinguish four virulence levels, with most of the isolates revealing an intermediate to severe virulence phenotype. Regardless the clonal population structure of the E. amylovora associated to the outbreaks occurring in Portugal between 2010 and 2017, the different virulence phenotypes, suggests that E. amylovora may have been introduced at different instances into the country. This is the first study regarding E. amylovora in Portugal, and it discloses a novel CRISPR genotype for this bacterium.
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Affiliation(s)
- Rafael J. Mendes
- Faculty of Sciences of University of Porto, Porto, Portugal
- LAQV/REQUIMTE, Faculty of Sciences of University of Porto, Porto, Portugal
- CITAB—Centre for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
- CIBIO–Research Centre in Biodiversity and Genetic Resources, InBIO, Associated Laboratory, University of Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - João Pedro Luz
- QRural, Polytechnic Institute of Castelo Branco, School of Agriculture, Castelo Branco, Portugal
| | - Conceição Santos
- Faculty of Sciences of University of Porto, Porto, Portugal
- LAQV/REQUIMTE, Faculty of Sciences of University of Porto, Porto, Portugal
| | - Fernando Tavares
- Faculty of Sciences of University of Porto, Porto, Portugal
- CIBIO–Research Centre in Biodiversity and Genetic Resources, InBIO, Associated Laboratory, University of Porto, Campus Agrário de Vairão, Vairão, Portugal
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Kałużna M, Albuquerque P, Tavares F, Sobiczewski P, Puławska J. Development of SCAR markers for rapid and specific detection of Pseudomonas syringae pv. morsprunorum races 1 and 2, using conventional and real-time PCR. Appl Microbiol Biotechnol 2016; 100:3693-711. [PMID: 26830104 PMCID: PMC4803819 DOI: 10.1007/s00253-016-7295-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/16/2015] [Accepted: 12/26/2015] [Indexed: 11/18/2022]
Abstract
Specific primers were developed to detect the causal agent of stone fruit bacterial canker using conventional and real-time polymerase chain reaction (PCR) methods. PCR melting profile (PCR MP) used for analysis of diversity of Pseudomonas syringae strains, allowed to pinpoint the amplified fragments specific for P. syringae pv. morsprunorum race 1 (Psm1) and race 2 (Psm2), which were sequenced. Using obtained data, specific sequence characterised amplified region (SCAR) primers were designed. Conventional and real-time PCRs, using genomic DNA isolated from different bacterial strains belonging to the Pseudomonas genus, confirmed the specificity of selected primers. Additionally, the specificity of the selected DNA regions for Psm1 and Psm2 was confirmed by dot blot hybridisation. Conventional and real-time PCR assays enabled accurate detection of Psm1 and Psm2 in pure cultures and in plant material. For conventional PCR, the detection limits were the order of magnitude ~10(0) cfu/reaction for Psm1 and 10(1) cfu/reaction for Psm2 in pure cultures, while in plant material were 10(0)-10(1) cfu/reaction using primers for Psm1 and 3 × 10(2) cfu/reaction using primers for Psm2. Real-time PCR assays with SYBR Green I showed a higher limit of detection (LOD) - 10(0) cfu/reaction in both pure culture and in plant material for each primer pairs designed, which corresponds to 30-100 and 10-50 fg of DNA of Psm1 and Psm2, respectively. To our knowledge, this is the first PCR-based method for detection of the causal agents of bacterial canker of stone fruit trees.
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Affiliation(s)
- Monika Kałużna
- Research Institute of Horticulture, Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland.
| | - Pedro Albuquerque
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
- Faculdade de Ciencias, Departamento de Biologia, Universidade do Porto, Edifício FC4, Via Panoramica No. 36, 4150-564, Porto, Portugal
| | - Fernando Tavares
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
- Faculdade de Ciencias, Departamento de Biologia, Universidade do Porto, Edifício FC4, Via Panoramica No. 36, 4150-564, Porto, Portugal
| | - Piotr Sobiczewski
- Research Institute of Horticulture, Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
| | - Joanna Puławska
- Research Institute of Horticulture, Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
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Scientific Opinion on the pest categorisation ofXanthomonas axonopodispv.phaseoliandXanthomonas fuscanssubsp.fuscans. EFSA J 2014. [DOI: 10.2903/j.efsa.2014.3856] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Boureau T, Kerkoud M, Chhel F, Hunault G, Darrasse A, Brin C, Durand K, Hajri A, Poussier S, Manceau C, Lardeux F, Saubion F, Jacques MA. A multiplex-PCR assay for identification of the quarantine plant pathogen Xanthomonas axonopodis pv. phaseoli. J Microbiol Methods 2012; 92:42-50. [PMID: 23142341 DOI: 10.1016/j.mimet.2012.10.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 10/25/2012] [Accepted: 10/28/2012] [Indexed: 11/26/2022]
Abstract
In this study we developed an algorithm to screen for all exact molecular signatures of the quarantine pathogen Xanthomonas axonopodis pv. phaseoli (Xap), based on available data of the presence or absence of virulence-associated genes. The simultaneous presence of genes avrBsT and xopL is specific to Xap. Therefore we developed a multiplex PCR assay targeting avrBsT and xopL for the molecular identification of Xap. The specificity of this multiplex was validated by comparison to that of other molecular identification assays aimed at Xap, on a wide collection of reference strains. This multiplex was further validated on a blind collection of Xanthomonas isolates for which pathogenicity was assayed by stem wounding and by dipping leaves into calibrated inocula. This multiplex was combined to the previously described X4c/X4e molecular identification assay for Xap. Such a combination enables the molecular identification of all strains of Xanthomonas pathogenic on bean. Results also show that assay by stem wounding does not give reliable results in the case of Xap, and that pathogenicity assays by dipping should be preferred.
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Affiliation(s)
- T Boureau
- Université d'Angers, UMR1345 IRHS, Institut de Recherches en Horticulture et Semences, SFR4207 QUASAV, PRES L'UNAM, F-49071 Beaucouze Cedex, France.
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Albuquerque P, Caridade CMR, Rodrigues AS, Marcal ARS, Cruz J, Cruz L, Santos CL, Mendes MV, Tavares F. Evolutionary and experimental assessment of novel markers for detection of Xanthomonas euvesicatoria in plant samples. PLoS One 2012; 7:e37836. [PMID: 22655073 PMCID: PMC3359998 DOI: 10.1371/journal.pone.0037836] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 04/25/2012] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Bacterial spot-causing xanthomonads (BSX) are quarantine phytopathogenic bacteria responsible for heavy losses in tomato and pepper production. Despite the research on improved plant spraying methods and resistant cultivars, the use of healthy plant material is still considered as the most effective bacterial spot control measure. Therefore, rapid and efficient detection methods are crucial for an early detection of these phytopathogens. METHODOLOGY In this work, we selected and validated novel DNA markers for reliable detection of the BSX Xanthomonas euvesicatoria (Xeu). Xeu-specific DNA regions were selected using two online applications, CUPID and Insignia. Furthermore, to facilitate the selection of putative DNA markers, a customized C program was designed to retrieve the regions outputted by both databases. The in silico validation was further extended in order to provide an insight on the origin of these Xeu-specific regions by assessing chromosomal location, GC content, codon usage and synteny analyses. Primer-pairs were designed for amplification of those regions and the PCR validation assays showed that most primers allowed for positive amplification with different Xeu strains. The obtained amplicons were labeled and used as probes in dot blot assays, which allowed testing the probes against a collection of 12 non-BSX Xanthomonas and 23 other phytopathogenic bacteria. These assays confirmed the specificity of the selected DNA markers. Finally, we designed and tested a duplex PCR assay and an inverted dot blot platform for culture-independent detection of Xeu in infected plants. SIGNIFICANCE This study details a selection strategy able to provide a large number of Xeu-specific DNA markers. As demonstrated, the selected markers can detect Xeu in infected plants both by PCR and by hybridization-based assays coupled with automatic data analysis. Furthermore, this work is a contribution to implement more efficient DNA-based methods of bacterial diagnostics.
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Affiliation(s)
- Pedro Albuquerque
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.
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